July 1, 2022

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Uncovering the genetics and early mode of transmission of Omicron

Nature: Uncovering the genetics and early mode of transmission of Omicron



 

Nature: Uncovering the genetics and early mode of transmission of Omicron

In a new study, researchers found that the Omicron  variant of SARS-CoV-2 is similar to the previous SARS- The divergence of CoV-2 variants is the result of adaptive evolution, in which beneficial mutations are passed on to offspring through natural selection rather than through recombination between previous variants.

The study is the first to characterize the genome of an Omicron variant and explore the origin of the variant.

Relevant research results were published online in the journal Nature on January 7, 2022, with the title of “Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa”.

 

“We saw that SARS-CoV-2 produced three major variants — Alpha, Delta, and Omicron — in about 16 months, which is very impressive,” said Maciej Boni, an associate professor of biology at Penn State and a co-author on the paper. Surprising, because other viruses don’t make such repeated big evolutionary jumps.

The latest variant — Omicron — is extraordinary because it made a bigger jump in the evolution of its spike protein. “

Nature: Uncovering the genetics and early mode of transmission of Omicron

 

Boni noted that compared to previous variants, the Omicron variant has more than 30 mutations in the spike protein, many of which are known to affect neutralization by host antibodies. “Given that the Omicron variant has taken such a big evolutionary leap, we wanted to investigate why and how this happened,” he said.

 

To do this, the team analyzed all 686 Omicron sequences as of December 7, 2021. They found that Omicron belonged to the B.1.1 lineage, as did the Alpha variant.

Interestingly, the team found that the Omicron variant is genetically distinct from the Alpha variant, as well as any other known variants of interest.

 

“This means that although the Omicron variant belongs to the same lineage as the Alpha variant, it has changed so much that it is largely unrecognizable as a cousin or nephew of the Alpha variant,” Boni said. When the Omicron genome was first sequenced, it became clear that the virus had the potential to be phenotypically very different from the SARS-CoV-2 variants we were previously familiar with.”

 

To determine when the Omicron variants first appeared, the team used a technique called time-calibrated Bayesian phylogenetic analysis. They estimate that the most recent common ancestor of all Omicron variants existed as early October 2021.

 

Next, the team performed selection analysis on 686 Omicron sequences and found evidence of positive natural selection for many genes since this variant diverged from other B.1.1 lineages. “This finding leads us to conclude that adaptive evolution played an important role in the early emergence and establishment of Omicron,” Boni said. “This finding suggests that Omicron is likely the result of an evolutionary process that created a A highly transmissible virus that has partially evaded our antibody response.”

 

Furthermore, this finding rules out that the origin of the Omicron variant is the result of recombination of previous variants. “We found no convincing evidence that the Omicron variant is a recombination of previous SARS-CoV-2 variants,” Boni said.

 

The team did find that some samples from Omicron showed weak evidence of inheriting genetic material from the Delta variant , but the statistical analysis couldn’t rule out random factors or small sequencing errors as the cause of this strange recombination signal.

 

“Given recent misinformation suggesting that the Omicron and Delta variants have recombined to create a super variant called ‘Deltacron’, it’s important to note that such recombination is in fact possible, but not currently available,” Boni said.

Evidence suggests that this has happened. Furthermore, if it does happen, it is not known what the properties of such a virus would be in terms of its ability to transmit and/or cause severe disease and other factors.”

 

Regarding the transmissibility of the Omicron variant, the team concluded that, given that the proportion of the South African population that is immune (whether from infection, vaccination, or both) is above 60%, partial immune evasion may be a factor in the rapid spread of Omicron in South Africa main driver.

 

Boni said, “This idea that Omicron can partially evade the immune system is supported by other recent findings showing an increased risk of SARS-CoV-2 reinfection associated with the presence of Omicron. We now know , Omicron’s viral load is higher in infected people, which also contributes to its high transmission rate.”

 

Boni noted that the current Omicron outbreak reminds all Americans to keep our COVID-19 vaccinations as high as possible. “We can’t afford another year of 500,000 deaths,” he said. 

 

 

Reference:

Raquel Viana et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, 2022, doi:10.1038/s41586-022-04411-y.

Nature: Uncovering the genetics and early mode of transmission of Omicron

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